Lyso-IP Organelle Specificity

Version: 1.0.0

Commit Hash: c8d7060ec511c069262d13d2c7ca9940498dbf9b

Author: CauldronGO Team

Category: lysoip-qc

Rewards a curated marker protein enriched toward IP, penalizes it more heavily if enriched toward WCL instead

Install with Cauldron get_app
README

Lyso-IP Organelle Specificity

Installation

⬇️ Click here to install in Cauldron (requires Cauldron to be running)

Repository: https://github.com/noatgnu/lysoip-organelle-specificity-plugin

Manual installation:

  1. Open Cauldron
  2. Go to Plugins → Install from Repository
  3. Paste: https://github.com/noatgnu/lysoip-organelle-specificity-plugin
  4. Click Install

ID: lysoip-organelle-specificity
Version: 1.0.0
Category: lysoip-qc
Author: CauldronGO Team

Description

Rewards a curated marker protein enriched toward IP, penalizes it more heavily if enriched toward WCL instead

Workflow Diagram

flowchart TD
    Start([Start]) --> step1
    step1["Loading organelle marker list"]
    step1 --> step2
    step2["Loading fold-change scores"]
    step2 --> step3
    step3["Writing organelle specificity scores"]
    step3 --> End([End])

Runtime

  • Environments: python

  • Entrypoint: lysoip_organelle_specificity.py

Inputs

Name Label Type Required Default Visibility
differential_expression_file Differential Expression file Yes - Always visible
organelle_list Expected Organelle List select (LSD (Platt 2018) (53 genes), Lysosome (Hein 2025) (158 genes), LSD + Lysosome (180 genes), ER (Hein 2025) (349 genes), Golgi (Hein 2025) (87 genes), Endosome (Park and Itzhak 2022) (93 genes), Mitochondria (Rath 2021) (1136 genes), Ribosome (Nakao 2004) (80 genes), Nucleus (Leung 2006) (410 genes)) Yes LSD + Lysosome Always visible
reward Reward number (min: 0, step: 0.1) No 1 Always visible
penalty Penalty number (min: 0, step: 0.1) No 2 Always visible

Input Details

Differential Expression (differential_expression_file)

differential_expression.tsv from the Lyso-IP Differential Expression plugin

Expected Organelle List (organelle_list)

Curated marker-gene list bundled with this plugin, converted from lysoip_qc_framework's Curated Organelle Protein Lists.xlsx

  • Options: LSD (Platt 2018) (LSD (Platt 2018) (53 genes)), Lysosome (Hein 2025) (Lysosome (Hein 2025) (158 genes)), LSD + Lysosome (LSD + Lysosome (180 genes)), ER (Hein 2025) (ER (Hein 2025) (349 genes)), Golgi (Hein 2025) (Golgi (Hein 2025) (87 genes)), Endosome (Park and Itzhak 2022) (Endosome (Park and Itzhak 2022) (93 genes)), Mitochondria (Rath 2021) (Mitochondria (Rath 2021) (1136 genes)), Ribosome (Nakao 2004) (Ribosome (Nakao 2004) (80 genes)), Nucleus (Leung 2006) (Nucleus (Leung 2006) (410 genes))

Reward (reward)

Multiplier applied to abs(fold_change) for a marker enriched toward IP

Penalty (penalty)

Multiplier applied to abs(fold_change) for a marker enriched toward WCL instead

Outputs

Name File Type Format Description
organelle_specificity organelle_specificity.tsv data tsv Per-protein organelle specificity score for marker genes only (non-members are untested, not zero)

Requirements

  • Python Version: >=3.11

Example Data

This plugin includes example data for testing:

  organelle_list: LSD + Lysosome
  differential_expression_file: examples/differential_expression.tsv

Load example data by clicking the Load Example button in the UI.

Usage

Via UI

  1. Navigate to lysoip-qc → Lyso-IP Organelle Specificity
  2. Fill in the required inputs
  3. Click Run Analysis

Via Plugin System

const jobId = await pluginService.executePlugin('lysoip-organelle-specificity', {
  // Add parameters here
});